diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml index 172de6f3..b6940123 100644 --- a/.github/workflows/clean-up.yml +++ b/.github/workflows/clean-up.yml @@ -10,7 +10,7 @@ jobs: issues: write pull-requests: write steps: - - uses: actions/stale@b5d41d4e1d5dceea10e7104786b73624c18a190f # v10 + - uses: actions/stale@4391f3da665fdf50b6810c1a66712fb9ba21aa93 # v11 with: stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 42b9f187..924b3afd 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -39,15 +39,15 @@ jobs: needs: configure steps: - name: Check out pipeline code - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 + uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 - name: Install Nextflow - uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 - name: Disk space cleanup uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6 + - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7 with: python-version: "3.14" architecture: "x64" diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml index 9262f8a8..dff65f48 100644 --- a/.github/workflows/fix_linting.yml +++ b/.github/workflows/fix_linting.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 with: token: ${{ secrets.nf_core_bot_auth_token }} @@ -32,12 +32,12 @@ jobs: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} - name: Install Nextflow - uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 # Install and run prek - name: Run prek id: prek - uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2 + uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2 continue-on-error: true # indication that the linting has finished diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index bc32219b..277f12fb 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -11,30 +11,30 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 - name: Install Nextflow - uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 - name: Run prek - uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2 + uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2 nf-core: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 + uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 - name: Install Nextflow - uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 + uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3 - - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6 + - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7 with: python-version: "3.14" architecture: "x64" - name: Setup uv - uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 + uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0 - name: read .nf-core.yml uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0 @@ -46,7 +46,7 @@ jobs: run: uv tool install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} - name: Run nf-core pipelines lint - if: ${{ github.base_ref != 'master' || github.base_ref != 'main' }} + if: ${{ github.base_ref != 'master' && github.base_ref != 'main' }} env: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/template-version-comment.yml b/.github/workflows/template-version-comment.yml index ee102f71..149e2851 100644 --- a/.github/workflows/template-version-comment.yml +++ b/.github/workflows/template-version-comment.yml @@ -12,7 +12,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 + uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7 with: ref: ${{ github.event.pull_request.head.sha }} diff --git a/.hooks/block_pipeline_outdir.sh b/.hooks/block_pipeline_outdir.sh new file mode 100755 index 00000000..e9ba4f93 --- /dev/null +++ b/.hooks/block_pipeline_outdir.sh @@ -0,0 +1,44 @@ +#!/usr/bin/env bash +# This hook is used to block commits if they include staged files inside a directory +# which also contains a subdirectory called `pipeline_info`. The purpose of this is to +# prevent users from inadvertently committing output from pipeline test runs inside the +# development directory. + +set -e + +status=0 +seen_dirs="" + +while IFS= read -r file; do + # The offending output bundle's root is the ancestor directory that has + # `pipeline_info` as an immediate child, so callers can restore it in one go. + if [[ "$file" == pipeline_info/* ]]; then + top_dir="pipeline_info" + elif [[ "$file" == */pipeline_info/* ]]; then + top_dir="${file%%/pipeline_info/*}" + else + top_dir="" + dir=$(dirname "$file") + while [[ "$dir" != "." && "$dir" != "/" ]]; do + if [[ -d "$dir/pipeline_info" ]]; then + top_dir="$dir" + break + fi + dir=$(dirname "$dir") + done + fi + + if [[ -n "$top_dir" ]]; then + echo "❌ Commit blocked: Please do not commit output from pipeline test runs to the pipeline code itself: $file" + status=1 + case "$seen_dirs" in + *"|$top_dir|"*) ;; + *) + echo "Run 'git restore --staged $top_dir' to remove the whole output folder from the staging area." + seen_dirs="$seen_dirs|$top_dir|" + ;; + esac + fi +done < <(git diff --cached --name-only) + +exit "$status" diff --git a/.nf-core.yml b/.nf-core.yml index 213c021c..35ec2941 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -39,7 +39,7 @@ lint: container_configs: false nf_test_content: - tests/gpu.nf.test -nf_core_version: 4.0.3 +nf_core_version: 4.1.0 repository_type: pipeline template: author: Anthony Gagnon diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 37e9b072..520ea4c2 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -9,7 +9,7 @@ repos: hooks: - id: prettier additional_dependencies: - - prettier@3.8.3 + - prettier@3.9.6 - repo: https://github.com/pre-commit/pre-commit-hooks rev: v6.0.0 hooks: @@ -30,9 +30,26 @@ repos: subworkflows/(?!local/).*| .*\.snap$ )$ + - id: check-added-large-files + args: [--maxkb=5000] + exclude: | + (?x)^( + .*ro-crate-metadata.json$| + .*\.snap$| + lib/nfcore_external_java_deps.jar$| + docs/.*\.(svg|pdf)$| + assets/.*$ + )$ + - id: check-merge-conflict - repo: https://github.com/seqeralabs/nf-lint-pre-commit rev: v0.3.0 hooks: - id: nextflow-lint files: '\.nf$|nextflow\.config$' args: ["-output", "json"] + - repo: local + hooks: + - id: block-pipeline-outdir + name: Prevent committing output from pipeline test runs to the pipeline code itself + entry: ./.hooks/block_pipeline_outdir.sh + language: script diff --git a/CHANGELOG.md b/CHANGELOG.md index b895b899..de1fa011 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -25,6 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` +- Update to nf-core template `4.1.0` ([#129](https://github.com/scilus/sf-pediatric/pull/129)) - Update to nf-core template `4.0.3` ([#127](https://github.com/scilus/sf-pediatric/pull/127)) - Move to parameter typing and bump minimal nextflow version to `26.04.0` ([#122](https://github.com/scilus/sf-pediatric/pull/122)) - Update to nf-core template `4.0.2` ([#117](https://github.com/scilus/sf-pediatric/pull/117)) diff --git a/CITATIONS.md b/CITATIONS.md index 4fc0d304..153ede98 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -1,4 +1,4 @@ -# scilus/sf-pediatric: Citations +# scilus/sf_pediatric: Citations ## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/) diff --git a/README.md b/README.md index 56dc62bd..8041cb1b 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ [![Static Badge](https://img.shields.io/badge/bioarXiv-10?style=flat&logo=arxiv&logoColor=%23B31B1B&label=10.64898%2F2026.01.19.700454&color=%23B31B1B&link=https%3A%2F%2Fdoi.org%2F10.64898%2F2026.01.19.700454)](https://doi.org/10.64898/2026.01.19.700454) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A526.04.0-23aa62.svg)](https://www.nextflow.io/) -[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1) +[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.1.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.1.0) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) diff --git a/conf/containers_conda_lock_files_amd64.config b/conf/containers_conda_lock_files_amd64.config index f487ba40..eb32fe50 100644 --- a/conf/containers_conda_lock_files_amd64.config +++ b/conf/containers_conda_lock_files_amd64.config @@ -1 +1 @@ -process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt' } } +process { withName: 'MULTIQC' { conda = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt' } } diff --git a/conf/containers_conda_lock_files_arm64.config b/conf/containers_conda_lock_files_arm64.config index e9a3fedc..3733ddfd 100644 --- a/conf/containers_conda_lock_files_arm64.config +++ b/conf/containers_conda_lock_files_arm64.config @@ -1 +1 @@ -process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt' } } +process { withName: 'MULTIQC' { conda = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt' } } diff --git a/conf/containers_docker_amd64.config b/conf/containers_docker_amd64.config index 01b59df5..ea18c3f9 100644 --- a/conf/containers_docker_amd64.config +++ b/conf/containers_docker_amd64.config @@ -1 +1 @@ -process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6' } } +process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc' } } diff --git a/conf/containers_docker_arm64.config b/conf/containers_docker_arm64.config index 7785cb13..369f743a 100644 --- a/conf/containers_docker_arm64.config +++ b/conf/containers_docker_arm64.config @@ -1 +1 @@ -process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136' } } +process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--5c84a5000a226ab5' } } diff --git a/conf/containers_singularity_https_amd64.config b/conf/containers_singularity_https_amd64.config index 754821b3..932fc7c0 100644 --- a/conf/containers_singularity_https_amd64.config +++ b/conf/containers_singularity_https_amd64.config @@ -1 +1 @@ -process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data' } } +process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data' } } diff --git a/conf/containers_singularity_https_arm64.config b/conf/containers_singularity_https_arm64.config index 93071de8..4f795323 100644 --- a/conf/containers_singularity_https_arm64.config +++ b/conf/containers_singularity_https_arm64.config @@ -1 +1 @@ -process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data' } } +process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e4/e48aa28aebc881254a499b24c3e1ce77b8df1b85a5432699ed6f72eb17ac7fb5/data' } } diff --git a/conf/containers_singularity_oras_amd64.config b/conf/containers_singularity_oras_amd64.config index 952881d8..2fa065b3 100644 --- a/conf/containers_singularity_oras_amd64.config +++ b/conf/containers_singularity_oras_amd64.config @@ -1 +1 @@ -process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0' } } +process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--c680f2aea25ccec2' } } diff --git a/conf/containers_singularity_oras_arm64.config b/conf/containers_singularity_oras_arm64.config index 498ec506..84f07924 100644 --- a/conf/containers_singularity_oras_arm64.config +++ b/conf/containers_singularity_oras_arm64.config @@ -1 +1 @@ -process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726' } } +process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--c0468833d65b2f81' } } diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md index b21ee385..2f413986 100644 --- a/docs/CONTRIBUTING.md +++ b/docs/CONTRIBUTING.md @@ -85,7 +85,7 @@ Please also refer to the [pipeline-specific contribution guidelines](#pipeline-s - [ ] Perform local tests to validate that the new code works as expected. - [ ] If applicable, add a new test in the `tests` directory. - [ ] Update `usage.md`, `output.md`, and `citation.md` as appropriate. -- [ ] [Lint](lint) the code with nf-core/tools. +- [ ] [Lint](#lint-tests) the code with nf-core/tools. - [ ] Update any diagrams or pipeline images as necessary. - [ ] Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name cleanup, and module plots are in the appropriate order. - [ ] If applicable, create a [MultiQC](https://seqera.io/multiqc/) module. @@ -123,7 +123,7 @@ Specify these with generic `withLabel:` selectors, so they can be shared across nf-core provides a set of standard labels that you should follow where possible, as seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config). These labels define resource defaults for single-core processes, modules that require a GPU, and different levels of multi-core configurations with increasing memory requirements. -Values assigned within these labels can be dynamically passed to a tool using the the `${task.cpus}` and `${task.memory}` Nextflow variables in the `script:` block of a module (see an example in the [modules repository](https://github.com/nf-core/modules/blob/bd1b6a40f55933d94b8c9ca94ec8c1ea0eaf4b82/modules/nf-core/samtools/bam2fq/main.nf#L30)). +Values assigned within these labels can be dynamically passed to a tool using the `${task.cpus}` and `${task.memory}` Nextflow variables in the `script:` block of a module (see an example in the [modules repository](https://github.com/nf-core/modules/blob/bd1b6a40f55933d94b8c9ca94ec8c1ea0eaf4b82/modules/nf-core/samtools/bam2fq/main.nf#L30)). #### Nextflow version bumping diff --git a/docs/output.md b/docs/output.md index 57075423..0e24d224 100644 --- a/docs/output.md +++ b/docs/output.md @@ -80,4 +80,4 @@ Within each subject folder, you will find subject-specific HTML reports. Those w -[Nextflow](https://www.nextflow.io/docs/latest/tracing.html) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage. +[Nextflow](https://docs.seqera.io/platform-cloud/reports/overview) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage. diff --git a/modules.json b/modules.json index 1eb7a6dc..0d0ebb94 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "multiqc": { "branch": "master", - "git_sha": "008f9d3e61209bf995edac3ba531f54e269e1215", + "git_sha": "98403d15b0e50edae1f3fec5eae5e24982f1fade", "installed_by": ["modules"] } } @@ -16,7 +16,7 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "1a545fcbd762911c21a64ced3dbef99b2b51ac75", + "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { diff --git a/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt b/modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt new file mode 100644 index 00000000..2a91c22d --- /dev/null +++ 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bioconda::multiqc=1.35 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 7a9f45a7..d0f928e0 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -4,8 +4,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data' - : 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data' + : 'community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc'}" input: tuple val(meta), path(multiqc_files, stageAs: "?/*"), path(multiqc_config, stageAs: "?/*"), path(multiqc_logo), path(replace_names), path(sample_names) diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index 2facc627..27ce18d8 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -110,24 +110,24 @@ maintainers: containers: conda: linux/amd64: - lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt + lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt linux/arm64: - lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt + lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt docker: linux/amd64: - name: community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6 - build_id: bd-db7c73dae76bc9e6_1 - scan_id: sc-66fc7138dbf1cf48_1 + name: community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc + build_id: bd-c17fb751507e9dfc_1 + scan_id: sc-3b1b3932f9846892_1 linux/arm64: - name: community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136 - build_id: bd-d167b8012595a136_1 - scan_id: sc-ac701dfa631a2af9_1 + name: community.wave.seqera.io/library/multiqc:1.35--5c84a5000a226ab5 + build_id: bd-5c84a5000a226ab5_1 + scan_id: sc-0d39df41e9737bbd_1 singularity: linux/amd64: - name: oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0 - build_id: bd-4fc8657c816047c0_1 - https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data + name: oras://community.wave.seqera.io/library/multiqc:1.35--c680f2aea25ccec2 + build_id: bd-c680f2aea25ccec2_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data linux/arm64: - name: oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726 - build_id: bd-7fbd82d945c06726_1 - https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data + name: oras://community.wave.seqera.io/library/multiqc:1.35--c0468833d65b2f81 + build_id: bd-c0468833d65b2f81_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e4/e48aa28aebc881254a499b24c3e1ce77b8df1b85a5432699ed6f72eb17ac7fb5/data diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 7c2f370f..44899216 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -81,7 +81,7 @@ [ "MULTIQC", "multiqc", - "1.34" + "1.35" ] ] } @@ -175,7 +175,7 @@ [ "MULTIQC", "multiqc", - "1.34" + "1.35" ] ] } @@ -221,7 +221,7 @@ [ "MULTIQC", "multiqc", - "1.34" + "1.35" ] ] } @@ -314,7 +314,7 @@ [ "MULTIQC", "multiqc", - "1.34" + "1.35" ] ] } @@ -408,7 +408,7 @@ [ "MULTIQC", "multiqc", - "1.34" + "1.35" ] ] } diff --git a/nextflow.config b/nextflow.config index 0d179240..d12611d1 100644 --- a/nextflow.config +++ b/nextflow.config @@ -240,13 +240,13 @@ params { trace_report_suffix = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') // Config options - config_profile_name = null - config_profile_description = null + config_profile_name = null + config_profile_description = null - custom_config_version = 'master' - custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" - config_profile_contact = null - config_profile_url = null + custom_config_version = 'master' + custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" + config_profile_contact = null + config_profile_url = null // Lean output mode. lean_output = true diff --git a/nextflow_schema.json b/nextflow_schema.json index 7467ba7f..a77ba925 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -65,8 +65,8 @@ "type": "string", "description": "Email address for completion summary.", "fa_icon": "fas fa-envelope", - "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.", "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$", + "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.", "hidden": true }, "multiqc_title_subject": { diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index d789dea0..5317cfd8 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -23,7 +23,7 @@ "@type": "Dataset", "creativeWorkStatus": "Stable", "datePublished": "2026-06-18T00:51:23+00:00", - "description": "# sf-pediatric\n\n[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/scilus/sf-pediatric)\n[![GitHub Actions CI Status](https://github.com/scilus/sf-pediatric/actions/workflows/nf-test.yml/badge.svg?branch=main)](https://github.com/scilus/sf-pediatric/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/scilus/sf-pediatric/actions/workflows/linting.yml/badge.svg?branch=main)](https://github.com/scilus/sf-pediatric/actions/workflows/linting.yml)\n[![Deploy documentation](https://github.com/scilus/sf-pediatric/actions/workflows/deploy.yml/badge.svg?branch=main)](https://github.com/scilus/sf-pediatric/actions/workflows/deploy.yml)\n[![Static Badge](https://img.shields.io/badge/bioarXiv-10?style=flat&logo=arxiv&logoColor=%23B31B1B&label=10.64898%2F2026.01.19.700454&color=%23B31B1B&link=https%3A%2F%2Fdoi.org%2F10.64898%2F2026.01.19.700454)](https://doi.org/10.64898/2026.01.19.700454)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A526.04.0-23aa62.svg)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n\n## Introduction\n\n**sf-pediatric** is an end-to-end age-adaptable pipeline for pediatric (0-18 years old) diffusion MRI. It leverages normative models of the brain diffusivities to perform connectomics analysis, WM bundles extraction and tractometry. Each pipeline run is wrapped in an interactive quality control reports for easy quality control of the processed data.\n\n![sf-pediatric-schema](/assets/sf-pediatric-schema.png)\n\n## Why sf-pediatric?\n\n**sf-pediatric** is an intelligent diffusion MRI pipeline that actively adapts to the rapidly evolving pediatric brain:\n\n- **Age-Adaptable**: Leverages normative trajectories from nearly 2,000 participants across six cohorts to dynamically adjust diffusion priors, template selection, and WM atlases based on each subject's age\n- **Birth to Adulthood**: Designed specifically for the 0-18 year age range, addressing the unique challenges of processing the developmental brain\n- **Rigorously Tested**: Demonstrates improved local modeling, cortical fanning, and robust recovery of known developmental trajectories of white matter microstructure\n- **Reproducible & Transparent**: Containerized workflows (Docker/Singularity) ensure consistent results across computing environments, with comprehensive quality control reports for every processing step\n- **Scalable & Portable**: Built with Nextflow for seamless deployment on cloud platforms, HPC clusters, or local computers\u2014ideal for large-scale pediatric neuroimaging studies\n- **Fully Automated**: End-to-end processing from raw acquisitions to statistics-ready datasets with integrated quality control reports\n- **Modular Workflows**: Four specialized profiles (tracking, segmentation, connectomics, bundling) tailored to your research question. Combined, these profiles allow you to:\n - Preprocess your diffusion and anatomical data.\n - Fit local models\n - Perform whole-brain tractography\n - White matter bundles extraction with tractometry\n - Cortical/Subcortical segmentation\n - Structural connectome analysis\n\n## Use Cases\n\n**sf-pediatric** is designed for researchers investigating:\n\n- White matter development and maturation trajectories\n- Structural brain connectivity across the developmental age-range\n- Neurodevelopmental disorders\n- Effects of early-life environmental factors on brain development\n- Normative vs. atypical brain development patterns\n- Large-scale multi-site pediatric neuroimaging studies\n- ...and much more!\n\n## Quick Start\n\nVisit our documentation at https://scilus.github.io/sf-pediatric/ for detailed instructions on organizing inputs, launching the pipeline, and analyzing results.\n\n**Encounter an issue?** Open an issue on GitHub!\n\n## Contributions and Support\n\nContributions welcome! See our [contributing guidelines](.github/CONTRIBUTING.md).\n\n**sf-pediatric** was originally written by Anthony Gagnon.\n\n## Citations\n\n**Methods boilerplate**. sf-pediatric provides a boilerplate methods section available in the QC reports. Users are encouraged to use this boilerplate in their publication. For a complete guide on how to navigate the reports, please [refer to the documentation](https://scilus.github.io/sf-pediatric/guides/qc).\n\nGagnon, A., Bor\u00e9, A., Valcourt Caron, A., Edde, M., Thoumyre, S., Lepage, J.-F., Talati, A., Posner, J., Ouellet, A., Brunet, M. A., Takser, L., Rheault, F., & Descoteaux, M. (2026). sf-pediatric: A robust and age-adaptable end-to-end pipeline for pediatric diffusion MRI. bioRxiv. https://doi.org/10.64898/2026.01.19.700454\n\n## License\n\nThis pipeline is released under the **MIT License**. See [LICENSE](LICENSE) for full details.\n\nThis pipeline uses code and infrastructure developed by the [nf-core](https://nf-co.re) community (MIT license) and incorporates tools from [nf-neuro](https://github.com/scilus/nf-neuro).\n", + "description": "# sf-pediatric\n\n[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/scilus/sf-pediatric)\n[![GitHub Actions CI Status](https://github.com/scilus/sf-pediatric/actions/workflows/nf-test.yml/badge.svg?branch=main)](https://github.com/scilus/sf-pediatric/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/scilus/sf-pediatric/actions/workflows/linting.yml/badge.svg?branch=main)](https://github.com/scilus/sf-pediatric/actions/workflows/linting.yml)\n[![Deploy documentation](https://github.com/scilus/sf-pediatric/actions/workflows/deploy.yml/badge.svg?branch=main)](https://github.com/scilus/sf-pediatric/actions/workflows/deploy.yml)\n[![Static Badge](https://img.shields.io/badge/bioarXiv-10?style=flat&logo=arxiv&logoColor=%23B31B1B&label=10.64898%2F2026.01.19.700454&color=%23B31B1B&link=https%3A%2F%2Fdoi.org%2F10.64898%2F2026.01.19.700454)](https://doi.org/10.64898/2026.01.19.700454)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A526.04.0-23aa62.svg)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.1.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.1.0)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n\n## Introduction\n\n**sf-pediatric** is an end-to-end age-adaptable pipeline for pediatric (0-18 years old) diffusion MRI. It leverages normative models of the brain diffusivities to perform connectomics analysis, WM bundles extraction and tractometry. Each pipeline run is wrapped in an interactive quality control reports for easy quality control of the processed data.\n\n![sf-pediatric-schema](/assets/sf-pediatric-schema.png)\n\n## Why sf-pediatric?\n\n**sf-pediatric** is an intelligent diffusion MRI pipeline that actively adapts to the rapidly evolving pediatric brain:\n\n- **Age-Adaptable**: Leverages normative trajectories from nearly 2,000 participants across six cohorts to dynamically adjust diffusion priors, template selection, and WM atlases based on each subject's age\n- **Birth to Adulthood**: Designed specifically for the 0-18 year age range, addressing the unique challenges of processing the developmental brain\n- **Rigorously Tested**: Demonstrates improved local modeling, cortical fanning, and robust recovery of known developmental trajectories of white matter microstructure\n- **Reproducible & Transparent**: Containerized workflows (Docker/Singularity) ensure consistent results across computing environments, with comprehensive quality control reports for every processing step\n- **Scalable & Portable**: Built with Nextflow for seamless deployment on cloud platforms, HPC clusters, or local computers\u2014ideal for large-scale pediatric neuroimaging studies\n- **Fully Automated**: End-to-end processing from raw acquisitions to statistics-ready datasets with integrated quality control reports\n- **Modular Workflows**: Four specialized profiles (tracking, segmentation, connectomics, bundling) tailored to your research question. Combined, these profiles allow you to:\n - Preprocess your diffusion and anatomical data.\n - Fit local models\n - Perform whole-brain tractography\n - White matter bundles extraction with tractometry\n - Cortical/Subcortical segmentation\n - Structural connectome analysis\n\n## Use Cases\n\n**sf-pediatric** is designed for researchers investigating:\n\n- White matter development and maturation trajectories\n- Structural brain connectivity across the developmental age-range\n- Neurodevelopmental disorders\n- Effects of early-life environmental factors on brain development\n- Normative vs. atypical brain development patterns\n- Large-scale multi-site pediatric neuroimaging studies\n- ...and much more!\n\n## Quick Start\n\nVisit our documentation at https://scilus.github.io/sf-pediatric/ for detailed instructions on organizing inputs, launching the pipeline, and analyzing results.\n\n**Encounter an issue?** Open an issue on GitHub!\n\n## Contributions and Support\n\nContributions welcome! See our [contributing guidelines](.github/CONTRIBUTING.md).\n\n**sf-pediatric** was originally written by Anthony Gagnon.\n\n## Citations\n\n**Methods boilerplate**. sf-pediatric provides a boilerplate methods section available in the QC reports. Users are encouraged to use this boilerplate in their publication. For a complete guide on how to navigate the reports, please [refer to the documentation](https://scilus.github.io/sf-pediatric/guides/qc).\n\nGagnon, A., Bor\u00e9, A., Valcourt Caron, A., Edde, M., Thoumyre, S., Lepage, J.-F., Talati, A., Posner, J., Ouellet, A., Brunet, M. A., Takser, L., Rheault, F., & Descoteaux, M. (2026). sf-pediatric: A robust and age-adaptable end-to-end pipeline for pediatric diffusion MRI. bioRxiv. https://doi.org/10.64898/2026.01.19.700454\n\n## License\n\nThis pipeline is released under the **MIT License**. See [LICENSE](LICENSE) for full details.\n\nThis pipeline uses code and infrastructure developed by the [nf-core](https://nf-co.re) community (MIT license) and incorporates tools from [nf-neuro](https://github.com/scilus/nf-neuro).\n", "hasPart": [ { "@id": "main.nf" diff --git a/subworkflows/local/utils_nfcore_sf_pediatric_pipeline/main.nf b/subworkflows/local/utils_nfcore_sf_pediatric_pipeline/main.nf index e8bc99d6..3c180e59 100644 --- a/subworkflows/local/utils_nfcore_sf_pediatric_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_sf_pediatric_pipeline/main.nf @@ -1460,11 +1460,11 @@ def buildMethodsDescription() { segmentation: { -> if ( !enabled('segmentation') ) return "" def parts = [] - parts << """
Cortical and sub-cortical segmentation
""" - parts << "Cortical and subcortical segmentation and surface reconstruction was performed using ${params.method == "fastsurfer" ? "FastSurfer (Henschel et al., 2020)" : params.method == "recon-all" ? " recon-all from FreeSurfer (Fischl, 2012)" : "recon-all-clinical from Freesurfer (Fischl, 2012; Billot et al., 2023; Iglesias et al., 2023)"} on the T1w anatomical images." - parts << "For younger participants (< 1 year old), cortical and subcortical segmentation was performed initially using BIBSnet (Hendrickson et al., 2026). Then, the BIBSnet segmentation was added as input to infant-recon-all to generate the final surfaces and cortical segmentation (Zöllei et al., 2020)." - parts << "Following segmentation, the ${params.atlas_name == "BrainnetomeChild" ? "Brainnetome atlas for preadolescents (Li et al., 2023)" : "${params.atlas_name} atlas"} was mapped from fsLR-32k space to subject-space using surface-based registration methods from FreeSurfer (Fischl, 2012) and then converted into voxel labels." - parts << "Volume, surface area, and cortical thickness were measured for each parcel and outputted in tab-separated value files." + parts << """
Cortical and subcortical segmentation
""" + parts << "Cortical/subcortical segmentation and surface reconstruction was performed using ${params.method == "fastsurfer" ? "FastSurfer (Henschel et al., 2020)" : params.method == "recon-all" ? " recon-all from FreeSurfer (Fischl, 2012)" : "recon-all-clinical from FreeSurfer (Fischl, 2012; Billot et al., 2023; Iglesias et al., 2023)"} on the T1-weighted anatomical images." + parts << "For younger participants (< 1 year old), cortical and subcortical segmentation was initially performed using BIBSnet (Hendrickson et al., 2026). The BIBSnet segmentation was then provided as input to infant-recon-all to generate the final cortical surfaces and segmentation (Zollei et al., 2020)." + parts << "Following segmentation, the ${params.atlas_name == "BrainnetomeChild" ? "Brainnetome atlas for preadolescents (Li et al., 2023)" : "${params.atlas_name} atlas"} was mapped from fsLR-32k space to subject space using surface-based registration methods from FreeSurfer (Fischl, 2012) and the connectome workbench (Marcus et al., 2011)." + parts << "Resulting labels were subsequently converted to voxel-wise labels. Volume, surface area, and cortical thickness were measured for each parcel and reported in tab-separated value (TSV) files." return parts.findAll{ it }.join(' ') }, @@ -1571,7 +1571,8 @@ def toolBibliographyText() { "Pasternak et al., 2009" : "
  • Pasternak, O., Sochen, N., Gur, Y., Intrator, N., & Assaf, Y. (2009). Free water elimination and mapping from diffusion MRI. Magnetic Resonance in Medicine, 62(3), 717–730. https://doi.org/10.1002/mrm.22055
    • ", "Renauld et al., 2026" : "
  • Renauld, E., Boré, A., Poirier, C., Valcourt-Caron, A., Karan, P., Théberge, A., Théaud, G., Edde, M., Poulin, P., Girard, G., Houde, J.-C., Gagnon, A., St-Onge, E., Little, G., Legarreta, J. H., Thoumyre, S., Grenier, G., El Yamani, Z., Ocampo Pineda, M., … Descoteaux, M. (2026). Tractography analysis with the scilpy toolbox. Aperture Neuro, 6. https://doi.org/10.52294/001c.154022
    • ", "Hendrickson et al., 2026" : "
  • Hendrickson, T. J., Reiners, P., Moore, L. A., Lundquist, J. T., Fayzullobekova, B., Perrone, A. J., Lee, E. G., Moser, J., Day, T. K. M., Alexopoulos, D., Styner, M., Kardan, O., Chamberlain, T. A., Mummaneni, A., Caldas, H. A., Bower, B., Stoyell, S., Martin, T., Sung, S., … Feczko, E. (2026). BIBSNet: A deep learning baby image brain segmentation network for MRI scans. Developmental Cognitive Neuroscience, 79, 101706. https://doi.org/10.1016/j.dcn.2026.101706
    • ", - "Zöllei et al., 2020" : "
  • Zöllei, L., Iglesias, J. E., Ou, Y., Grant, P. E., & Fischl, B. (2020). Infant FreeSurfer: An automated segmentation and surface extraction pipeline for T1-weighted neuroimaging data of infants 0–2 years. NeuroImage, 218, 116946. https://doi.org/10.1016/j.neuroimage.2020.116946
    • ", + "Zollei et al., 2020" : "
  • Zöllei, L., Iglesias, J. E., Ou, Y., Grant, P. E., & Fischl, B. (2020). Infant FreeSurfer: An automated segmentation and surface extraction pipeline for T1-weighted neuroimaging data of infants 0–2 years. NeuroImage, 218, 116946. https://doi.org/10.1016/j.neuroimage.2020.116946
    • ", + "Marcus et al., 2011" : "
  • Marcus, D. S., Harwell, J., Olsen, T., Hodge, M., Glasser, M. F., Prior, F., Jenkinson, M., Laumann, T., Curtiss, S. W., & Van Essen, D. C. (2011). Informatics and data mining tools and strategies for the human connectome project. Frontiers in Neuroinformatics, 5, 4. https://doi.org/10.3389/fninf.2011.00004
    • ", // Preprints and in-preparation works "Gagnon et al., 2026" : "
  • Gagnon, A., Boré, A., Valcourt Caron, A., Edde, M., Thoumyre, S., Lepage, J.-F., Talati, A., Posner, J., Ouellet, A., Brunet, M. A., Takser, L., Rheault, F., & Descoteaux, M. (2026). sf-pediatric: A robust and age-adaptable end-to-end pipeline for pediatric diffusion MRI. bioRxiv. https://doi.org/10.64898/2026.01.19.700454
    • ", ] diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index 37939acd..d6e593e8 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -73,23 +73,11 @@ def getWorkflowVersion() { def dumpParametersToJSON(outdir) { def timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss') def filename = "params_${timestamp}.json" - def temp_pf = workflow.launchDir.resolve(".${filename}") - def jsonGenerator = new groovy.json.JsonGenerator.Options() - .excludeNulls() - .addConverter(Path) { Path path -> path.toUriString() } - .addConverter(Duration) { Duration duration -> duration.toMillis() } - .addConverter(MemoryUnit) { MemoryUnit memory -> memory.toBytes() } - .addConverter(nextflow.script.types.VersionNumber) { nextflow.script.types.VersionNumber version -> version.toString() } - .build() - def jsonStr = jsonGenerator.toJson(params) + def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") + def jsonStr = groovy.json.JsonOutput.toJson(params) temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr) - if (outdir instanceof Path) { - temp_pf.copyTo(outdir.resolve("pipeline_info/${filename}")) - } else if (outdir instanceof String) { - temp_pf.copyTo("${outdir}/pipeline_info/params_${timestamp}.json") - } else { - log.warn("Could not determine type of outdir, parameters JSON file will not be copied to output directory!") - } + + nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") temp_pf.delete() }